Chip-scale photonics has emerged as an exciting field which can potentially solve many of the problems plaguing the high-performance computing industry, from large-scale to embedded. In theory, photonics is a superior communication medium because of its higher bandwidth density using wave-division multiplexing and bandwidth-power translucency to distance traveled. In practice, physical-layer design and engineering issues such as optical loss, crosstalk, and packaging have slowed its entry into widespread adoption at the chip and board scale. In this work, we present these issues and potential design improvements. The major contributions, however, are the tools and methods we have developed for the design of photonic interconnection networks, including a system-level simulator and CAD and modeling environment for layout, both of which are publicly available to the research community.